\name{circos.genomicText}
\alias{circos.genomicText}
\title{
Draw text in a cell, specifically for genomic graphics
}
\description{
Draw text in a cell, specifically for genomic graphics
}
\usage{
circos.genomicText(
    region,
    value = NULL,
    y = NULL,
    labels = NULL,
    labels.column = NULL,
    numeric.column = NULL,
    sector.index = get.current.sector.index(),
    track.index = get.current.track.index(),
    posTransform = NULL,
    direction = NULL,
    facing = "inside",
    niceFacing = FALSE,
    adj = par("adj"),
    cex = 1,
    col = "black",
    font = par("font"),
    padding = 0,
    extend = 0,
    align_to = "region",
    ...)
}
\arguments{

  \item{region}{A data frame contains 2 column which correspond to start positions and end positions.}
  \item{value}{A data frame contains values and other information.}
  \item{y}{A vector or a single value indicating position of text.}
  \item{labels}{Labels of text corresponding to each genomic positions.}
  \item{labels.column}{If labels are in \code{value}, index of column in \code{value}.}
  \item{numeric.column}{Which column in \code{value} data frame should be taken as y-value. If it is not defined, only the first numeric columns in \code{value} will be taken.}
  \item{sector.index}{Index of sector.}
  \item{track.index}{Index of track.}
  \item{posTransform}{Self-defined function to transform genomic positions, see \code{\link{posTransform.default}} for explanation.}
  \item{facing}{Passing to \code{\link{circos.text}}. Settings are similar as \code{col}.}
  \item{niceFacing}{Should the facing of text be adjusted to fit human eyes?}
  \item{direction}{Deprecated, use \code{facing} instead. }
  \item{adj}{Pass to \code{\link{circos.text}}. Settings are similar as \code{col}.}
  \item{cex}{Pass to \code{\link{circos.text}}. Settings are similar as \code{col}.}
  \item{col}{Pass to \code{\link{circos.text}}. The length of \code{col} can be either one or number of rows of \code{region}.}
  \item{font}{Pass to \code{\link{circos.text}}. Settings are similar as \code{col}.}
  \item{padding}{pass to \code{posTransform} if it is set as \code{\link{posTransform.text}}.}
  \item{extend}{pass to \code{posTransform} if it is set as \code{\link{posTransform.text}}.}
  \item{align_to}{pass to \code{posTransform} if it is set as \code{\link{posTransform.text}}.}
  \item{...}{Mysterious parameters.}

}
\details{
The function is a low-level graphical function and usually is put in \code{panel.fun} when using \code{\link{circos.genomicTrack}}.
}
\examples{
circos.par("track.height" = 0.1, cell.padding = c(0, 0, 0, 0))
circos.initializeWithIdeogram(plotType = NULL)

bed = generateRandomBed(nr = 20)

circos.genomicTrack(bed, ylim = c(0, 1), panel.fun = function(region, value, ...) {
    circos.genomicText(region, value, y = 0.5, labels = "text", ...)
})

bed = cbind(bed, sample(letters, nrow(bed), replace = TRUE))
circos.genomicTrack(bed, panel.fun = function(region, value, ...) {
    circos.genomicText(region, value, labels.column = 2, ...)
})

circos.clear()
}
